[gmx-users] How to center my trimer in my simulation box.

[Ilya Chorny]

Just to clarify.
I would run

trjconv -f *.gro -s *.tpr -pbc nojump -o out.gro?

What would I run next?

Thanks,

Ilya


On Tue, Apr 22, 2008 at 2:59 PM, Xavier Periole <X.Periole at rug.nl> wrote:

> On Tue, 22 Apr 2008 14:14:19 -0700
>  "Ilya Chorny" <ichorny at gmail.com> wrote:
>
> > Hello,
> >
> > I am simulating a trimer in a membrane. In one of my simulation  two of
> > the
> > monomers are on one side of the box and the other monomer is on the
> > other
> > side of the box. I tried using trjconv to center the whole thing in the
> > center of my simulation cell but have failed miserably. I also searched
> > around for about an hour and could not find anything.
> >
> > I use trjconv -f *.gro -s *.tpr -center rect -pbc whole -o *.gro.
> >
> first run
> trjconv -pbc nojump
>
> > Any advice?
> >
> > Thanks,
> >
> > Ilya
> >
> > --
> > Ilya Chorny Ph.D.
> >
>
> -----------------------------------------------------
> XAvier Periole - PhD
>
> NMR & Molecular Dynamics Group
> University of Groningen
> The Netherlands
> http://md.chem.rug.nl/~periole
> -----------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Ilya Chorny Ph.D.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080422/87e6bef3/attachment.html>